| Title | Authors | Type | Link |
|---|---|---|---|
| Cluster 1 | |||
| DiffER: Categorical Diffusion Models for Chemical Retrosynthesis | Sean Current ... srinivasan parthasarathy | Accept | Open Paper |
| Homomorphism Counts as Structural Encodings for Molecular Property Prediction | Linus Bao ... Matthias Lanzinger | Accept | Open Paper |
| SmileyLlama: Modifying Large Language Models \\for Directed Chemical Space Exploration | Joe Cavanagh ... Thomas D. Bannister | Accept | Open Paper |
| An Efficient Tokenization for Molecular Language Models | Seojin Kim ... Jinwoo Shin | Accept | Open Paper |
| Chain-of-thoughts for molecular understanding | Yunhui Jang ... Sungsoo Ahn | Accept | Open Paper |
| Cluster 2 | |||
| Deep Interactions for Multimodal Molecular Property Prediction | Patrick Soga ... Jundong Li | Accept | Open Paper |
| Geometry-text Multi-modal Foundation Model for Reactivity-oriented Molecule Editing | Haorui Li ... Anima Anandkumar | Accept | Open Paper |
| 3D Interaction Geometric Pre-training for Molecular Relational Learning | Namkyeong Lee ... Chanyoung Park | Accept | Open Paper |
| GFlowNet Pretraining with Inexpensive Rewards | Mohit Pandey ... Emmanuel Bengio | Accept | Open Paper |
| MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction | Liang Zeng | Accept | Open Paper |
| Molphenix: A Multimodal Foundation Model for PhenoMolecular Retrieval | Philip Fradkin ... Dominique Beaini | Accept | Open Paper |
| Learning Molecular Representation in a Cell | Gang Liu ... Shantanu Singh | Accept | Open Paper |
| Understanding the Sources of Performance in Deep Drug Response Models Reveals Insights and Improvements | Nikhil Branson ... Conrad Bessant | Accept | Open Paper |
| Reinforcement Learning for Enhanced Targeted Molecule Generation Via Language Models | Salma J. Ahmed, Emad A. Mohammed | Accept | Open Paper |
| SMORE-DRL: Scalable Multi-Objective Robust and Efficient Deep Reinforcement Learning for Molecular Optimization | Aws Al Jumaily ... Yifeng Li | Accept | Open Paper |
| Pharmacophore-based design by learning on voxel grids | Omar Mahmood ... Vishnu Sresht | Accept | Open Paper |
| MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning | Peter Eckmann ... Rose Yu | Accept | Open Paper |
| GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking | Yiliang Yuan, Mustafa Misir | Accept | Open Paper |
| Similarity-Quantized Relative Difference Learning for Improved Molecular Activity Prediction | Karina Zadorozhny ... Colin A Grambow | Accept | Open Paper |
| Cluster 3 | |||
| Improved Off-policy Reinforcement Learning in Biological Sequence Design | Hyeonah Kim ... Jinkyoo Park | Accept | Open Paper |
| Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design | Chenyu Wang ... Aviv Regev | Accept | Open Paper |
| Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding | Xiner Li ... Masatoshi Uehara | Accept | Open Paper |
| Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion | Anirban Sarkar ... Peter K Koo | Accept | Open Paper |
| Latent Diffusion Models for Controllable RNA Sequence Generation | Kaixuan Huang ... Mengdi Wang | Accept | Open Paper |
| Cluster 4 | |||
| Modeling Complex System Dynamics with Flow Matching Across Time and Conditions | Martin Rohbeck ... Romain Lopez | Accept | Open Paper |
| Correlational Lagrangian Schrodinger Bridge: Learning Dynamics with Population-Level Regularization | Yuning You ... Yang Shen | Accept | Open Paper |
| Cluster 5 | |||
| Training-Free Guidance with Applications to Protein Engineering | Lewis Cornwall ... Aaron Sim | Accept | Open Paper |
| ProtPainter: Draw or Drag Protein via Topology-guided Diffusion | Zhengxi Lu ... Min Zhang | Accept | Open Paper |
| TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation | Zongying Lin ... Yonghong Tian | Accept | Open Paper |
| Structure Language Models for Protein Conformation Generation | Jiarui Lu ... Jian Tang | Accept | Open Paper |
| MeMDLM: De Novo Membrane Protein Design with Masked Discrete Diffusion Protein Language Models | Shrey Goel ... Pranam Chatterjee | Accept | Open Paper |
| Improving Antibody Design with Force-Guided Sampling in Diffusion Models | Paulina Kulytė ... Pietro Lio | Accept | Open Paper |
| JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling | Ameya Daigavane ... Joseph Kleinhenz | Accept | Open Paper |
| Learning Protocols for Non-Equilibrium Conformational Free-Energy Estimation Using Optimal Transport and Conditional Flow Matching | Lars Holdijk ... Max Welling | Accept | Open Paper |
| Generalized Flow Matching for Transition Dynamics Modeling | Haibo Wang ... Yuanqi Du | Accept | Open Paper |
| Cluster 6 | |||
| A Deep Generative Model for the Design of Synthesizable Ionizable Lipids | Yuxuan Ou ... José Miguel Hernández-Lobato | Accept | Open Paper |
| Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree Search Approach | Jingyi Zhao ... José Miguel Hernández-Lobato | Accept | Open Paper |
| Cluster 7 | |||
| Discrete Diffusion Schrödinger Bridge Matching for Graph Transformation | Jun Hyeong Kim ... Woo Youn Kim | Accept | Open Paper |
| Improving Molecular Graph Generation with Flow Matching and Optimal Transport | Xiaoyang Hou ... Shiwei Sun | Accept | Open Paper |
| Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models | Jeff Guo, Philippe Schwaller | Spotlight | Open Paper |
| Generative Flows on Synthetic Pathway for Drug Design | Seonghwan Seo ... Woo Youn Kim | Accept | Open Paper |
| Molecular Generation with State Space Sequence Models | Anri Lombard ... Jan Buys | Accept | Open Paper |
| Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation | Jeff Guo, Philippe Schwaller | Accept | Open Paper |
| Best Practices for Multi-Fidelity Bayesian Optimization in Materials and Molecular Research | Victor Sabanza Gil ... Loïc Roch | Accept | Open Paper |
| MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks | Nayoung Kim ... Sungsoo Ahn | Accept | Open Paper |
| Improving Structural Plausibility in 3D Molecule Generation via Property-Conditioned Training with Distorted Molecules | Lucy Vost ... Charlotte Deane | Accept | Open Paper |
| Applications of Modular Co-Design for De Novo 3D Molecule Generation | Danny Reidenbach ... Saee Gopal Paliwal | Accept | Open Paper |
| Cluster 8 | |||
| Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+ | Ethan Weinberger ... Ryan Conrad | Accept | Open Paper |
| Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all | Ihab Bendidi ... Alisandra Kaye Denton | Accept | Open Paper |
| PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis | Yan Wu ... Thore Graepel | Spotlight | Open Paper |
| PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction | Aaron Wenteler ... César Miguel Valdez Córdova | Accept | Open Paper |
| Weighted Diversified Sampling for Efficient Data-Driven Single-Cell Gene-Gene Interaction Discovery | Yifan Wu ... Zhaozhuo Xu | Accept | Open Paper |
| Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space | Jason Qin ... Yuhan Hao | Accept | Open Paper |
| CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer | Alexander Theus ... Valentina Boeva | Accept | Open Paper |
| Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics | Alejandro Velez-Arce ... Marinka Zitnik | Spotlight | Open Paper |
| Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states | Tianyu Liu ... Graham Heimberg | Accept | Open Paper |
| Scaling Dense Representations for Single Cell Gene Expression with Transcriptome-Scale Context | Nicholas Ho ... Eric P. Xing | Accept | Open Paper |
| Cell ontology guided transcriptome foundation model | Xinyu Yuan ... Jian Tang | Accept | Open Paper |
| Cluster 9 | |||
| Video Representation Learning of Cardiac MRI for Genetic Discovery | Matt Sooknah ... Jun Xu | Accept | Open Paper |
| Representation Learning based Target Discovery from UKBB MRI data | Sivaramakrishnan Sankarapandian ... Jun Xu | Accept | Open Paper |
| Cluster 10 | |||
| Foundational Model-aided Automatic High-throughput Drug Screening Using Self-controlled Cohort Study | Shenbo Xu ... Kenney Ng | Accept | Open Paper |
| TrialDura: Hierarchical Attention Transformer for Interpretable Clinical Trial Duration Prediction | Ling Yue ... Tianfan Fu | Accept | Open Paper |
| Interpretable Causal Representation Learning for Biological Data in the Pathway Space | Jesus de la Fuente Cedeño ... Mikel Hernaez | Accept | Open Paper |
| Learning to refine domain knowledge for biological network inference | Peiwen Li, Menghua Wu | Accept | Open Paper |
| FluxGAT: Integrating Flux Sampling with Graph Neural Networks for Unbiased Gene Essentiality Classification | Kieren Sharma ... Lucia Marucci | Accept | Open Paper |
| Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph | Kexin Huang ... Jure Leskovec | Accept | Open Paper |
| Leveraging Disease-Specific Topologies and Counterfactual Relationships in Knowledge Graphs for Inductive Reasoning in Drug Repurposing | Cerag Oguztuzun ... Rong Xu | Spotlight | Open Paper |
| A Foundational Multi-Modal Knowledge Graph for Pancreatic Cancer Drug Effects Prediction | Jingwen Hui ... Anima Anandkumar | Accept | Open Paper |
| Cluster 11 | |||
| TCRGenesis: Generation of SIINFEKL-specific T-cell receptor sequences using autoregressive Transformer | Yang An ... Benjamin Schubert | Accept | Open Paper |
| Modeling CAR Response at the Single-Cell Level Using Conditional OT | Alice Driessen ... Marianna Rapsomaniki | Accept | Open Paper |
| Disentangling the Peptide Space: A Contrastive Approach with Wasserstein Autoencoders | Mihir Agarwal, Progyan Das | Accept | Open Paper |
| Epitope Generation for Peptide-based Cancer Vaccine using Goal-directed Wasserstein Generative Adversarial Network with Gradient Penalty | Yen-Che Hsiao, Abhishek Dutta | Accept | Open Paper |
| Cluster 12 | |||
| LLMs are Highly-Constrained Biophysical Sequence Optimizers | Angelica Chen ... Nathan C. Frey | Spotlight | Open Paper |
| Language Models for Text-guided Protein Evolution | Zhanghan Ni ... Anima Anandkumar | Accept | Open Paper |
| Distilling Structural Representations into Protein Sequence Models | Jeffrey Ouyang-Zhang ... Daniel Jesus Diaz | Accept | Open Paper |
| LatentDE: Latent-based Directed Evolution accelerated by Gradient Ascent for Protein Sequence Design | Thanh V. T. Tran ... Truong Son Hy | Accept | Open Paper |
| PLMFit: Benchmarking Transfer Learning with Protein Language Models for Protein Engineering | Thomas Bikias ... Sai T. Reddy | Accept | Open Paper |
| Harnessing Preference Optimisation in Protein LMs for Hit Maturation in Cell Therapy | Katarzyna Janocha ... Nils Yannick Hammerla | Accept | Open Paper |
| Alignment-based and protein foundation models for viral evolution, vaccines and vectors | Sarah Gurev ... Debora Susan Marks | Spotlight | Open Paper |
| Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs | Talip Ucar ... Ferran Gonzalez | Accept | Open Paper |
| EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics | Chenqing Hua ... Shuangjia Zheng | Accept | Open Paper |
| Evaluating synergies among generative design models for multi-objective optimization of drug-like proteins | Jung-Eun Shin ... Ryan Peckner | Accept | Open Paper |
| Machine learning enables engineering of potent, specific, and therapeutically developable proteases | Jung-Eun Shin ... Ryan Peckner | Accept | Open Paper |
| IgBlend: Unifying 3D Structure and Sequence for Antibody LLMs | Cedric Malherbe, Talip Ucar | Spotlight | Open Paper |
| Antibody Library Design by Seeding Linear Programming with Inverse Folding and Protein Language Models | Conor F. Hayes ... Mikel Landajuela | Accept | Open Paper |
| Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences | Alan Nawzad Amin ... Andrew Gordon Wilson | Spotlight | Open Paper |
| Computational Antigen Optimization through Symbolic Optimization and Affinity Maturation Simulation | Jonathan G. Faris ... Felipe Leno da Silva | Spotlight | Open Paper |
| Cluster 13 | |||
| DeepADAR: A deep learning approach to model regulatory elements of ADAR-based RNA editing and its application to gRNA design | Andrew J Jung ... Brendan Frey | Spotlight | Open Paper |
| Detection of RNA Editing Sites by GPT Fine-tuning | Zohar Rosenwasser ... Gal Oren | Accept | Open Paper |
| Mixture of Experts Enable Efficient and Effective Protein Understanding and Design | Ning Sun ... Eric P. Xing | Spotlight | Open Paper |
| A Large-Scale Foundation Model for RNA Function and Structure Prediction | Shuxian Zou ... Eric P. Xing | Spotlight | Open Paper |
| Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale | Caleb Ellington ... Le Song | Accept | Open Paper |
| Orthrus: Towards Evolutionary and Functional RNA Foundation Models | Philip Fradkin ... BO WANG | Spotlight | Open Paper |
| HELM: Hierarchical Encoding for mRNA Language Modeling | Mehdi Yazdani-Jahromi ... Rui Liao | Accept | Open Paper |
| Beyond Sequence: Impact of Geometric Context for RNA Property Prediction | Junjie Xu ... Rui Liao | Accept | Open Paper |
| ML-driven design of 3’ untranslated regions for mRNA stability | Alyssa Kramer Morrow ... Uri Laserson | Accept | Open Paper |
| Cluster 14 | |||
| AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions | Wei Lu ... Shuangjia Zheng | Accept | Open Paper |
| BindingGYM: A Large-Scale Mutational Dataset Toward Deciphering Protein-Protein Interactions | Wei Lu ... Shuangjia Zheng | Accept | Open Paper |
| A Deep Learning Approach for RNA-Compound Interaction Prediction with Binding Site Interpretability | Haelee Bae, Hojung Nam | Spotlight | Open Paper |
| AptaBLE: A Deep Learning Platform for SELEX Optimization | Sawan Patel ... Sherwood Yao | Accept | Open Paper |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Jiaqing Xie ... Tianfan Fu | Spotlight | Open Paper |
| Understanding Protein-DNA Interactions by Paying Attention to Protein and Genomics Foundation Models | Dhruva Rajwade ... Anima Anandkumar | Accept | Open Paper |
| Cluster 15 | |||
| Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo | Jun Xia ... Stan Z. Li | Spotlight | Open Paper |
| Effective Protein-Protein Interaction Exploration with PPIretrieval | Chenqing Hua ... Shuangjia Zheng | Accept | Open Paper |
| PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models | Eli M Carrami, Sahand Sharifzadeh | Spotlight | Open Paper |
| GeneGench: Systematic Evaluation of Genomic Foundation Models and Beyond | Zicheng Liu ... Stan Z. Li | Accept | Open Paper |
| Diverse Genomic Embedding Benchmark for functional evaluation across the tree of life. | Jacob West-Roberts ... Yunha Hwang | Accept | Open Paper |
| MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model | Sumin Ha ... Sun Kim | Accept | Open Paper |
| Natural Language Prompts Guide the Design of Novel Functional Protein Sequences | Niksa Praljak ... Andrew Ferguson | Accept | Open Paper |
| Probing the Embedding Space of Protein Foundation Models through Intrinsic Dimension Analysis | Soojung Yang ... Rafael Gomez-Bombarelli | Accept | Open Paper |
| PepDoRA: A Unified Peptide Language Model via Weight-Decomposed Low-Rank Adaptation | Leyao Wang ... Pranam Chatterjee | Accept | Open Paper |